Archaeopteryx

Overview

Archaeopteryx (Google+) is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees.
Archaeopteryx (the successor to ATV) is entirely written in the Java programming language (it is based on the forester libraries). It can be used both as a standalone application and aapplet (ArchaeopteryxA and ArchaeopteryxE).

Launching Archaeopteryx

Windows

Clicking on the "forester.jar" file should start it, the configuration file
("_aptx_configuration_file") will be used if it is in the same directory as the jar
file.

Unix, Linux, Windows

command line (without use of a configuration file or "_aptx_configuration_file" is
in the same directory as the jar file):
"java -cp path\to\forester.jar
org.forester.archaeopteryx.Archaeopteryx"

command line for using a configuration file anywhere in the file system:
"java -cp path\to\forester.jar org.forester.archaeopteryx.Archaeopteryx -c
path\to\_aptx_configuration_file"

command line for directly opening a treefile and using a configuration file
anywhere in the file system:
"java -cp path\to\forester.jar org.forester.archaeopteryx.Archaeopteryx -c
path\to\_aptx_configuration_file treefile"

Increasing memory

Since the Java default memory allocation is quite small, it might by necessary (for
trees with more than around 5000 external nodes) to increase the memory which Java
can use, with "-Xmx" Java command line option.
For example:
"java -Xmx2048m -cp path\to\forester.jar
org.forester.archaeopteryx.Archaeopteryx -c
path\to\_aptx_configuration_file"

Windows batch file

To avoid typing, it is easiest to create at batch (.bat) file. For example create a
new file named "aptx.bat" and put a line like this into it:java -Xmx2048m -cp "C:\path\to\forester.jar"
org.forester.archaeopteryx.Archaeopteryx -c
"C:\path\to\_aptx_configuration_file"
Clicking on "aptx.bat" should now start Archaeopteryx.

Examples

Archaeopteryx applets (ArchaeopteryxA, ArchaeopteryxE) require the Oracle Java plug-in. Most web browsers under Windows have this already installed. Under Linux, this plug-in might need to be installed, though. For example, under Mint or Ubuntu Linux, the Java plug-in can be downloaded and installed with the following command: "sudo apt-get install sun-java6-jre sun-java6-plugin".

Important note: While Archaeopteryx currently (May 2014) still allows input in NHX format, support for this format is expected to be removed in future versions. Therefore it is strongly recommended to prepare for migration to phyloXML (use phyloxml_converter with -f=dummy option to convert NHX formatted trees to phyloXML).

Source Code

The source code for Archaeopteryx (as application/module of the the open source
forester libraries) is available on GitHub.

Mailing List & Google+ Page

Please consider joining the Archaeopteryx Google Group and/or follow the Archaeopteryx Google+ page to
be informed of updates and changes (probably no more than about one message per week).